SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes

• Published in: BMC bioinformatics Vol. 9; no. 1; p. 536
• Main Authors: Lemoine, Frédéric, Labedan, Bernard, Lespinet, Olivier
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 16-12-2008; BioMed Central; BMC
• Subjects: Applications software; Biochemistry, Molecular Biology; Computational Biology - methods; Conserved Sequence; Databases, Genetic; DNA sequencing; Evolution, Molecular; Gene expression; Gene Order - genetics; Genetic aspects; Genome, Archaeal; Genome, Bacterial; Genomics - methods; Life Sciences; Methods; Nucleotide sequencing; Prokaryotes; Quantitative Methods; Software; Synteny - genetics; France
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-9-536

It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.
After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr.
SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.